rs12438387

Positions:

• chr15-47688828-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558014.5(SEMA6D):​c.-54-70917A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,022 control chromosomes in the GnomAD database, including 21,657 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.52 (21657 hom., cov: 32)
• Consequence: SEMA6D ENST00000558014.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827

Genes affected

SEMA6D (HGNC:16770): (semaphorin 6D) Semaphorins are a large family, including both secreted and membrane associated proteins, many of which have been implicated as inhibitors or chemorepellents in axon pathfinding, fasciculation and branching, and target selection. All semaphorins possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Additional sequence motifs C-terminal to the semaphorin domain allow classification into distinct subfamilies. Results demonstrate that transmembrane semaphorins, like the secreted ones, can act as repulsive axon guidance cues. This gene encodes a class 6 vertebrate transmembrane semaphorin that demonstrates alternative splicing. Several transcript variants have been identified and expression of the distinct encoded isoforms is thought to be regulated in a tissue- and development-dependent manner. [provided by RefSeq, Nov 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEMA6D	NM_001198999.2	c.-54-70917A>G		intron_variant			NP_001185928.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEMA6D	ENST00000558014.5	c.-54-70917A>G		intron_variant		1		ENSP00000452815	A1
SEMA6D	ENST00000559184.5	c.-54-70917A>G		intron_variant		4		ENSP00000453097
SEMA6D	ENST00000560636.5	c.-54-70917A>G		intron_variant		4		ENSP00000453420

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78858 AN: 151904 Hom.: 21646 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.513

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.519 AC: 78892 AN: 152022 Hom.: 21657 Cov.: 32 AF XY: 0.526 AC XY: 39050 AN XY: 74298

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.514

Alfa AF: 0.561 Hom.: 26635

Bravo AF: 0.496

Asia WGS AF: 0.569 AC: 1982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12438387; hg19: chr15-47981025;